"We have a privileged role in society but it comes at a cost," the commissioner said.

"This will continue to be one of our greatest challenges going forward."

Home Affairs Minister Peter Dutton praised the outgoing police chief.

"I thank Andrew for his inspirational leadership, diligence and hard work in protecting the community, and on behalf of all Australians, thank him for making Australia a safer place," Mr Dutton said.

Mr Colvin joined the AFP in 1990, spending most of his early career in Sydney investigating serious and organised crime.

He co-ordinated the AFP's response to the 2002 Bali bombings, along with two other deadly terror attacks in Jakarta.

Mr Colvin was awarded an Order of Australia for his efforts.

"I thank AFP Commissioner Andrew Colvin for his service and sacrifice - both as commissioner of the AFP for the past five years and his 30 year career in law enforcement," Labor's Kristina Keneally said.